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Bug Bulletin: The recent 3.2 release fixes many issues. If you run into a problem, please try the latest version before posting a bug report, as your problem may already have been solved.

# Error in VariantsToVCF

Posts: 2Member

Hi

I am trying to covert the UCSC format of SNP to VCF format. I downloaded dbSNP128.txt.gz from (UCSC http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/snp128.txt.gz). The command I used is java -jar GenomeAnalysisTK.jar -R mm9.fa -T VariantsToVCF --variant:OLDDBSNP dbSNP128.txt -o dbsnp128.vcf

Error message:

##### ERROR ------------------------------------------------------------------------------------------
• Posts: 6,046Administrator, GATK Developer admin

OK, thanks for trying. We'll need you to narrow down the error to the offending record and upload a snippet to our FTP server so that we can reproduce the error and fix the bug. Please see this article on how to do that:

http://www.broadinstitute.org/gatk/guide/article?id=1894

Geraldine Van der Auwera, PhD

• Posts: 2Member

Hi

Uploaded. File name is duanjl.bug.report.2013-1-16.tar.gz

Thanks.

• Posts: 2Member

I need to run the exact same command with dbSNP 132 for mm9. Has this fix been implemented in 2.3-9? If it isn't available til 2.4 then when will that be released?

-Phil

• Posts: 6,046Administrator, GATK Developer admin

We are finalizing the contents of 2.4 and are expecting to release next week if all goes well.

Geraldine Van der Auwera, PhD

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